The game loosely followed the plot of the then-recently released Star Trek Generations motion picture. Notable departures included an additional battle against Tholian forces, a Romulan ambush involving both space and ground combat at Amargosa Station, and a different resolution to the capture of Geordi La Forge.

The game combines three different styles of play with minor differences from level to level. Spaceflight is done in a primitive pseudo-3D environment. Players steer their ship from a first-person point of view, moving between markers or using phasers and later photon torpedoes to attack enemy vessels. On-foot levels are played from a top-down perspective and involve either phaser combat or labyrinth-like pathfinding. The remaining levels consist of simple puzzles such as symbol matching.

The Game Boy and Game Gear versions of the game are identical, save for their colour palette: while the GB version is limited to monochrome graphics (or a limited palette when played through a Super Game Boy adapter), the Game Gear version features full colour visuals.